Merge pull request #10 from scientificcomputing/intro

Intro

.gitignore

@@ -1,6 +1,6 @@
 # Created by https://www.toptal.com/developers/gitignore/api/python
 # Edit at https://www.toptal.com/developers/gitignore?templates=python
-docs/documentation.html
+docs/*.html
 _build
 ### Python ###
 # Byte-compiled / optimized / DLL files

README.md

@@ -18,3 +18,9 @@ The agenda is as follows
 - https://scientificcomputing.github.io
 - [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/reproducible-research)
 - [Scientific Python Library Development Guide](https://learn.scientific-python.org/development/)
+
+
+## Authors
+- Henrik Finsberg ([email protected])
+- Jørgen Dokken ([email protected])
+- Benjamin Ragan-Kelly ([email protected])

_config.yml

@@ -2,7 +2,8 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: BioAI Seminar
-author: Henrik Finsberg and Jørgen Dokken
+author: Henrik Finsberg, Jørgen Dokken and Benjamin Ragan-Kelly
+logo: "docs/logo.png"
 copyright: "2023"
 only_build_toc_files: true
 
@@ -36,5 +37,3 @@ sphinx:
   - 'sphinx.ext.autodoc'
   - 'sphinx.ext.napoleon'
   - 'sphinx.ext.viewcode'
-
-exclude_patterns: [".pytest_cache/*"]

docs/distribution.md

@@ -15,48 +15,4 @@ marp: true
 # Distribution
 Best Practices in Modern Software Development: 23.11.23
 
-Henrik Finsberg and Jørgen Dokken
-
----
-
-## Agenda
-
-- How to package a python project
-- Uploading a package to pypi
-    - Creating a GitHub action to publish a package on pypi whenever you make a new release
-- Uploading conda package to conda-forge
-- Creating and publishing docker images
-    - Creating a GitHub action to publish a new docker image to the GitHub registry whenever you make a new release
-- Licensing
-    - Which license to put on your code and why you should use a permissive license
-
----
-
-## Creating a package
-
-- A set of modules can be collected in a package
-
-- A package is organized as module files in a directory tree
-
-- Each subdirectory must have a __init__.py file (can be empty)
-
-```
-examples/my-package
-├── LICENSE
-├── pyproject.toml
-├── README.md
-├── src
-│   └── pkg
-│       ├── analysis.py
-│       ├── __init__.py
-│       └── printing
-│           ├── __init__.py
-│           └── printing.py
-└── test
-    ├── test_analysis.py
-    └── test_printing.py
-```
-
----
-
-## Installing a package
+To be included in a future version

docs/documentation.md

@@ -2,7 +2,7 @@
 theme: default
 paginate: true
 header: 'Best Practices in Modern Software Development: Documentation'
-footer: '23.11.23 - Henrik Finsberg and Jørgen Dokken'
+footer: '23.11.23 - Jørgen Dokken'
 size: 16:9
 style: |
   .small-text {

docs/environments.md

@@ -2,7 +2,7 @@
 theme: default
 paginate: true
 header: 'Best Practices in Modern Software Development: Reproducible environments'
-footer: '23.11.23 - Henrik Finsberg and Jørgen Dokken'
+footer: '23.11.23 - Benjamin Ragan-Kelly'
 size: 16:9
 style: |
   .small-text {

docs/paper.md

@@ -2,7 +2,7 @@
 theme: default
 paginate: true
 header: 'Best Practices in Modern Software Development: Paper with code'
-footer: '23.11.23 - Henrik Finsberg and Jørgen Dokken'
+footer: '23.11.23 - Henrik Finsberg'
 size: 16:9
 style: |
   .small-text {

docs/repo.md

@@ -2,7 +2,7 @@
 theme: default
 paginate: true
 header: 'Best Practices in Modern Software Development: Code and Data repositories'
-footer: '23.11.23 - Henrik Finsberg and Jørgen Dokken'
+footer: '23.11.23 - Henrik Finsberg'
 size: 16:9
 style: |
   .small-text {

intro.md

@@ -0,0 +1,48 @@
+---
+theme: default
+paginate: true
+header: 'Best Practices in Modern Software Development'
+footer: '23.11.23 - Henrik Finsberg'
+size: 16:9
+style: |
+  .small-text {
+    font-size: 0.55rem;
+  }
+html: true
+marp: true
+---
+
+# Elevating Scientific Computing at Simula: Best Practices in Modern Software Development.
+
+23.11.23
+
+Henrik Finsberg, Jørgen Dokken and Benjamin Ragan-Kelly
+
+---
+
+## Research at Simula is based on code
+
+* We write code to **pre-process** data
+* We write code to **run simulations**
+* We write code to create figures and tables (**post-processing**)
+
+* Whenever you publish a paper, you need to have recipe for how to reproduce the results in the paper
+
+---
+
+## Goal of this workshops
+
+- 11.15 - 11.45: Code and data repositories (Henrik)
+- 11.45 - 12.15: Reproducible environments (Min)
+- 12.15 - 12.45: Lunch
+- 12.45 - 13.15: Linters, formatters and continuous integration (Henrik + Jørgen)
+- 13.15 - 13.45: Documentation (Jørgen)
+- 13.45 - 14.00: Break
+- 14.00 - 14.30: A paper with code (Henrik)
+
+---
+
+## Material from the workshop
+
+- https://github.com/scientificcomputing/seminar-23-11-2023
+- https://scientificcomputing.github.io/seminar-23-11-2023/README.html